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I was wondering if the human body would be capable of functioning with, say, cellulolytic bacteria in their gut (instead of or in addition of their current bacteria), like that of ruminants and if they'd be able to digest cellulose thanks to it.
Couldn't find any papers on that, only on the implantation of faecal matter from a healthy gut to a sick one, nothing interspecific.
Evolutionary change in the human gut microbiome: From a static to a dynamic view
Our intestine is a melting pot of interactions between microbial and human cells. This gene-rich ecosystem modulates our health, but questions remain unanswered regarding its genetic structure, such as, “How rapid is evolutionary change in the human gut microbiome? How can its function be maintained?” Much research on the microbiome has characterized the species it contains. Yet the high growth rate and large population sizes of many species, and the mutation rate of most microbes (approximately 10 −3 per genome per generation), could imply that evolution might be happening in our gut along our lifetime. In support of this view, Garud and colleagues present an analysis that begins to unravel the pattern of short- and long-term evolution of dozens of gut species. Even with limited longitudinal short-read sequence data, significant evolutionary dynamics—shaped by both positive and negative selection—can be detected on human microbiomes. This may only be the tip of the iceberg, as recent work on mice suggests, and its full extent should be revealed with dense time series long-read sequence data and new eco-evolutionary theory.
Citation: Gordo I (2019) Evolutionary change in the human gut microbiome: From a static to a dynamic view. PLoS Biol 17(2): e3000126. https://doi.org/10.1371/journal.pbio.3000126
Published: February 7, 2019
Copyright: © 2019 Isabel Gordo. This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.
Funding: The author received no specific funding for this work.
Competing interests: The authors have declared that no competing interests exist.
Abbreviation: SNV, single nucleotide variant
Provenance: Commissioned externally peer reviewed.
What’s your gut type?
Artistic impression of the 3 human gut types. Image credits: EMBL/ P. Riedinger
In the future, when you walk into a doctor’s surgery or hospital, you could be asked not just about your allergies and blood group, but also about your gut type. Scientists at the European Molecular Biology Laboratory (EMBL) in Heidelberg, Germany, and collaborators in the international MetaHIT consortium, have found that humans have 3 different gut types. The study, published today in Nature, also uncovers microbial genetic markers that are related to traits like age, gender and body-mass index. These bacterial genes could one day be used to help diagnose and predict outcomes for diseases like colo-rectal cancer, while information about a person’s gut type could help inform treatment.
We all have bacteria in our gut that help digest food, break down toxins, produce some vitamins and essential amino acids, and form a barrier against invaders. But the composition of that microbial community – the relative numbers of different kinds of bacteria – varies from person to person.
“We found that the combination of microbes in the human intestine isn’t random,” says Peer Bork, who led the study at EMBL: “our gut flora can settle into three different types of community – three different ecosystems, if you like.”
Bork and colleagues first used stool samples to analyse the gut bacteria of 39 individuals from three different continents (Europe, Asia and America), and later extended the study to an extra 85 people from Denmark and 154 from America. They found that all these cases could be divided into three groups, based on which species of bacteria occurred in high numbers in their gut: each person could be said to have one of three gut types, or enterotypes.
The scientists don’t yet know why people have these different gut types, but speculate that they could be related to differences in how their immune systems distinguish between ‘friendly’ and harmful bacteria, or to different ways of releasing hydrogen waste from cells.
Like blood groups, these gut types are independent of traits like age, gender, nationality and body-mass index. But the scientists did find, for example, that the guts of older people appear to have more microbial genes involved in breaking down carbohydrates than those of youngsters, possibly because as we age we become less efficient at processing those nutrients, so in order to survive in the human gut, bacteria have to take up the task.
“The fact that there are bacterial genes associated with traits like age and weight indicates that there may also be markers for traits like obesity or diseases like colo-rectal cancer,” Bork says, “which could have implications for diagnosis and prognosis.”
If this proves to be the case, when diagnosing or assessing the likelihood of a patient contracting a particular disease, doctors could look for clues not only in the patient’s body but also in the bacteria that live in it. And after diagnosis, treatment could be adapted to the patient’s gut type to ensure the best results.
For more information:
About the human gut microbiome: EMBL press release: Bacterial balance that keeps us healthy
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How can lowly gut bacteria down there affect higher functions up there in the brain? How can unintelligent, simple organisms affect behaviors, thoughts, and actions of our intellect? These microbiotas have several strategies to affect our brains and therefore minds. One that has already been mentioned above is that gut bacteria produce neurotransmitters that are important for behaviors, mood, thoughts and other cognitive abilities.
Also, some microbiota can change how these brain chemicals get metabolized in the body and thus determine how much is available for action in blood circulation. Other chemicals generated by gut bacteria are called neuroactive, such as butyrate, which has been shown to reduce anxiety and depression. Another pathway is the vagus nerve which is one conduit for the bidirectional gut-brain communication (5). The immune system is yet another one. The immune system is intimately connected to the gut microbiome and the nervous system, and thus can be a mediator of the gut’s effects on the brain and the brain’s effects on the gut.
Not only have many studies across many laboratories showed evidence for brain-gut interactions, but scientists have also cataloged specific bacteria as they relate to various states of mental health. In a large population study (part of the Flemish Gut Flora project), researchers investigated the correlation between microbiome factors and quality of life and depression. Not only did they find a link between the gut microbiome and mental health, but they were able to catalog the exact names of bacteria associated with good and bad quality of life. (6)
What has become evident is that patients with psychiatric disorders have different populations of gut microbes compared to microbes in healthy individuals. Also, stress and stress hormones such as cortisol can have a negative impact on our microbiome. And all of these factors interact in complex ways with the immune system.
As the knowledge of the exact nature of brain-gut interactions unfolds in relation to psychiatric disorders, treatments may include a probiotic instead of Prozac! What all of the above findings strongly suggest is this: Take care of your gut bacteria for good quality of life, better mental health, and a sharper brain.
(1) Sternbach H, State R. Antibiotics: neuropsychiatric effects and psychotropic interactions. (1997). Harv Rev Psychiatry 5: 214–226.
(2) Whitehead WE, Palsson O, Jones KR. Systematic review of the comorbidity of irritable bowel syndrome with other disorders: what are the causes and implications? (2002). Gastroenterology, 122: 1140–1156.
(3) Tillisch, K., Labus, J., Kilpatrick, L., Jiang, Z., Stains, J., Ebrat, B., … Mayer, E. A. (2013). Consumption of fermented milk product with probiotic modulates brain activity. Gastroenterology, 144(7), 1394–1401.e14014. doi:10.1053/j.gastro.2013.02.043
(4) Pearson-Leary, J., Zhao, C., Bittinger, K., …Bhatnagar, S. (2019). The gut microbiome regulates the increase in depressive-type behaviors and in inflammatory processes in the ventral hippocampus of stress vulnerable rats. Molecular Psychiatry. https://doi.org/10.1038/s41380-019-0380-x
(5) Bravo, J. A., Forsythe, P., Chew, M.V., …Cryan, J.F. (2011). Ingestion of Lactobacillus strain regulates emotional behavior and central GABA receptor expression in a mouse via the vagus nerve. PNAS, 108(38), 16050-16055. https://doi.org/10.1073/pnas.1102999108
(6) Valles-Colomer, M., Falony, G., Darzi, Y., . Raes, J. (2019). The neuroactive potential of the human gut microbiota in quality of life and depression. Nature Microbiology, 4, 623-632.
In humans, the gut microbiota has the largest numbers of bacteria and the greatest number of species compared to other areas of the body.  In humans, the gut flora is established at one to two years after birth, by which time the intestinal epithelium and the intestinal mucosal barrier that it secretes have co-developed in a way that is tolerant to, and even supportive of, the gut flora and that also provides a barrier to pathogenic organisms.  
The relationship between some gut flora and humans is not merely commensal (a non-harmful coexistence), but rather a mutualistic relationship.  : 700 Some human gut microorganisms benefit the host by fermenting dietary fiber into short-chain fatty acids (SCFAs), such as acetic acid and butyric acid, which are then absorbed by the host.   Intestinal bacteria also play a role in synthesizing vitamin B and vitamin K as well as metabolizing bile acids, sterols, and xenobiotics.   The systemic importance of the SCFAs and other compounds they produce are like hormones and the gut flora itself appears to function like an endocrine organ,  and dysregulation of the gut flora has been correlated with a host of inflammatory and autoimmune conditions.  
The composition of human gut microbiota changes over time, when the diet changes, and as overall health changes.   A systematic review from 2016 examined the preclinical and small human trials that have been conducted with certain commercially available strains of probiotic bacteria and identified those that had the most potential to be useful for certain central nervous system disorders. 
The microbial composition of the gut microbiota varies across the digestive tract. In the stomach and small intestine, relatively few species of bacteria are generally present.   The colon, in contrast, contains the highest microbial density recorded in any habitat on Earth  with up to 10 12 cells per gram of intestinal content.  These bacteria represent between 300 and 1000 different species.   However, 99% of the bacteria come from about 30 or 40 species.  As a consequence of their abundance in the intestine, bacteria also make up to 60% of the dry mass of feces.  Fungi, protists, archaea, and viruses are also present in the gut flora, but less is known about their activities. 
Over 99% of the bacteria in the gut are anaerobes, but in the cecum, aerobic bacteria reach high densities.  It is estimated that these gut flora have around a hundred times as many genes in total as there are in the human genome. 
Many species in the gut have not been studied outside of their hosts because most cannot be cultured.    While there are a small number of core species of microbes shared by most individuals, populations of microbes can vary widely among different individuals.  Within an individual, microbe populations stay fairly constant over time, even though some alterations may occur with changes in lifestyle, diet and age.   The Human Microbiome Project has set out to better describe the microflora of the human gut and other body locations.
The four dominant bacterial phyla in the human gut are Firmicutes, Bacteroidetes, Actinobacteria, and Proteobacteria.  Most bacteria belong to the genera Bacteroides, Clostridium, Faecalibacterium,   Eubacterium, Ruminococcus, Peptococcus, Peptostreptococcus, and Bifidobacterium.   Other genera, such as Escherichia and Lactobacillus, are present to a lesser extent.  Species from the genus Bacteroides alone constitute about 30% of all bacteria in the gut, suggesting that this genus is especially important in the functioning of the host. 
Fungal genera that have been detected in the gut include Candida, Saccharomyces, Aspergillus, Penicillium, Rhodotorula, Trametes, Pleospora, Sclerotinia, Bullera, and Galactomyces, among others.   Rhodotorula is most frequently found in individuals with inflammatory bowel disease while Candida is most frequently found in individuals with hepatitis B cirrhosis and chronic hepatitis B. 
Archaea constitute another large class of gut flora which are important in the metabolism of the bacterial products of fermentation.
Industralization is associated with changes in the microbiota and the reduction of diversity could drive certain species to extinction in 2018, researchers proposed a biobank repository of human microbiota. 
An enterotype is a classification of living organisms based on its bacteriological ecosystem in the human gut microbiome not dictated by age, gender, body weight, or national divisions.  There are indications that long-term diet influences enterotype.  Three human enterotypes have been proposed,   but their value has been questioned. 
Due to the high acidity of the stomach, most microorganisms cannot survive there. The main bacterial inhabitants of the stomach include: Streptococcus, Staphylococcus, Lactobacillus, Peptostreptococcus.  : 720 Helicobacter pylori is a gram-negative spiral bacterium that establishes on gastric mucosa causing chronic gastritis, and peptic ulcer disease, and is a carcinogen for gastric cancer.  : 904
|Bacteria commonly found in the human colon |
The small intestine contains a trace amount of microorganisms due to the proximity and influence of the stomach. Gram-positive cocci and rod-shaped bacteria are the predominant microorganisms found in the small intestine.  However, in the distal portion of the small intestine alkaline conditions support gram-negative bacteria of the Enterobacteriaceae.  The bacterial flora of the small intestine aid in a wide range of intestinal functions. The bacterial flora provide regulatory signals that enable the development and utility of the gut. Overgrowth of bacteria in the small intestine can lead to intestinal failure.  In addition the large intestine contains the largest bacterial ecosystem in the human body.  About 99% of the large intestine and feces flora are made up of obligate anaerobes such as Bacteroides and Bifidobacterium.  Factors that disrupt the microorganism population of the large intestine include antibiotics, stress, and parasites. 
Bacteria make up most of the flora in the colon  and 60% of the dry mass of feces.  This fact makes feces an ideal source of gut flora for any tests and experiments by extracting the nucleic acid from fecal specimens, and bacterial 16S rRNA gene sequences are generated with bacterial primers. This form of testing is also often preferable to more invasive techniques, such as biopsies.
Five phyla dominate the intestinal microbiota: bacteroidetes, firmicutes, actinobacteria, proteobacteria, and verrucomicrobia—with bacteroidetes and firmicutes constituting 90% of the composition.  Somewhere between 300  and 1000 different species live in the gut,  with most estimates at about 500.   However, it is probable that 99% of the bacteria come from about 30 or 40 species, with Faecalibacterium prausnitzii (phylum firmicutes) being the most common species in healthy adults.  
Research suggests that the relationship between gut flora and humans is not merely commensal (a non-harmful coexistence), but rather is a mutualistic, symbiotic relationship.  Though people can survive with no gut flora,  the microorganisms perform a host of useful functions, such as fermenting unused energy substrates, training the immune system via end products of metabolism like propionate and acetate, preventing growth of harmful species, regulating the development of the gut, producing vitamins for the host (such as biotin and vitamin K), and producing hormones to direct the host to store fats.  Extensive modification and imbalances of the gut microbiota and its microbiome or gene collection are associated with obesity.  However, in certain conditions, some species are thought to be capable of causing disease by causing infection or increasing cancer risk for the host.  
Fungi and protists also make up a part of the gut flora, but less is known about their activities. 
It has been demonstrated that there are common patterns of microbiome composition evolution during life.  In general, the diversity of microbiota composition of fecal samples is significantly higher in adults than in children, although interpersonal differences are higher in children than in adults.  Much of the maturation of microbiota into an adult-like configuration happens during the three first years of life. 
As the microbiome composition changes, so does the composition of bacterial proteins produced in the gut. In adult microbiomes, a high prevalence of enzymes involved in fermentation, methanogenesis and the metabolism of arginine, glutamate, aspartate and lysine have been found. In contrast, in infant microbiomes the dominant enzymes are involved in cysteine metabolism and fermentation pathways. 
Studies and statistical analyses have identified the different bacterial genera in gut microbiota and their associations with nutrient intake. Gut microflora is mainly composed of three enterotypes: Prevotella, Bacteroides, and Ruminococcus. There is an association between the concentration of each microbial community and diet. For example, Prevotella is related to carbohydrates and simple sugars, while Bacteroides is associated with proteins, amino acids, and saturated fats. Specialist microbes that break down mucin survive on their host's carbohydrate excretions.  One enterotype will dominate depending on the diet. Altering the diet will result in a corresponding change in the numbers of species.  A 2021 study suggests that childhood diet and exercise can substantially affect adult microbiome composition and diversity. Its authors show that in mice a diet high in fat and sugar still substantially affects the gut microbiome after what equates to six human years.   
Vegetarian and vegan diets Edit
While plant-based diets have some variation, vegetarian and vegan diets patterns are the most common. Vegetarian diets exclude meat products (which include fish) but still allow for eggs and dairy, while vegan diets exclude all forms of animal products. The diets of vegetarian and vegan individuals create a microbiome distinct from meat eaters, however there is not a significant distinction between the two.  [ unreliable medical source? ] In diets that are centered around meat and animal products, there are high abundances of Alistipes, Bilophila and Bacteroides which are all bile tolerant and may promote inflammation in the gut. In this type of diet, the group Firmicutes, which is associated with the metabolism of dietary plant polysaccharides, is found in low concentrations.  Conversely, diets rich in plant-based materials are associated with greater diversity in the gut microbiome overall, and have a greater abundance of Prevotella, responsible for the long-term processing of fibers, rather than the bile tolerant species.  [ unreliable medical source? ] Diet can be used to alter the composition of the gut microbiome in relatively short timescales. However, if wanting to change the microbiome to combat a disease or illness, long-term changes in diet have proven to be most successful. 
Gut microbiome composition depends on the geographic origin of populations. Variations in a trade-off of Prevotella, the representation of the urease gene, and the representation of genes encoding glutamate synthase/degradation or other enzymes involved in amino acids degradation or vitamin biosynthesis show significant differences between populations from the US, Malawi or Amerindian origin. 
The US population has a high representation of enzymes encoding the degradation of glutamine and enzymes involved in vitamin and lipoic acid biosynthesis whereas Malawi and Amerindian populations have a high representation of enzymes encoding glutamate synthase and they also have an overrepresentation of α-amylase in their microbiomes. As the US population has a diet richer in fats than Amerindian or Malawian populations which have a corn-rich diet, the diet is probably the main determinant of the gut bacterial composition. 
Further studies have indicated a large difference in the composition of microbiota between European and rural African children. The fecal bacteria of children from Florence were compared to that of children from the small rural village of Boulpon in Burkina Faso. The diet of a typical child living in this village is largely lacking in fats and animal proteins and rich in polysaccharides and plant proteins. The fecal bacteria of European children were dominated by Firmicutes and showed a marked reduction in biodiversity, while the fecal bacteria of the Boulpon children was dominated by Bacteroidetes. The increased biodiversity and different composition of gut flora in African populations may aid in the digestion of normally indigestible plant polysaccharides and also may result in a reduced incidence of non-infectious colonic diseases. 
On a smaller scale, it has been shown that sharing numerous common environmental exposures in a family is a strong determinant of individual microbiome composition. This effect has no genetic influence and it is consistently observed in culturally different populations. 
Malnourished children have less mature and less diverse gut microbiota than healthy children, and changes in the microbiome associated with nutrient scarcity can in turn be a pathophysiological cause of malnutrition.   Malnourished children also typically have more potentially pathogenic gut flora, and more yeast in their mouths and throats.  Altering diet may lead to changes in gut microbiota composition and diversity. 
Race and ethnicity Edit
Researchers with the American Gut Project and Human Microbiome Project found that twelve microbe families varied in abundance based on the race or ethnicity of the individual. The strength of these associations is limited by the small sample size: the American Gut Project collected data from 1,375 individuals, 90% of whom were white.  The Healthy Life in an Urban Setting (HELIUS) study in Amsterdam found that those of Dutch ancestry had the highest level of gut microbiota diversity, while those of South Asian and Surinamese descent had the lowest diversity. The study results suggested that individuals of the same race or ethnicity have more similar microbiomes than individuals of different racial backgrounds. 
Socioeconomic status Edit
As of 2020, at least two studies have demonstrated a link between an individual's socioeconomic status (SES) and their gut microbiota. A study in Chicago found that individuals in higher SES neighborhoods had greater microbiota diversity. People from higher SES neighborhoods also had more abundant Bacteroides bacteria. Similarly, a study of twins in the United Kingdom found that higher SES was also linked with a greater gut diversity. 
The establishment of a gut flora is crucial to the health of an adult, as well as the functioning of the gastrointestinal tract.  In humans, a gut flora similar to an adult's is formed within one to two years of birth as microbiota are acquired through parent-to-child transmission and transfer from food, water, and other environmental sources.  
The traditional view of the gastrointestinal tract of a normal fetus is that it is sterile, although this view has been challenged in the past few years.  Multiple lines of evidence have begun to emerge that suggest there may be bacteria in the intrauterine environment. In humans, research has shown that microbial colonization may occur in the fetus  with one study showing Lactobacillus and Bifidobacterium species were present in placental biopsies.  Several rodent studies have demonstrated the presence of bacteria in the amniotic fluid and placenta, as well as in the meconium of babies born by sterile cesarean section.   In another study, researchers administered a culture of bacteria orally to a pregnant dam, and detected the bacteria in the offspring, likely resulting from transmission between the digestive tract and amniotic fluid via the blood stream.  However, researchers caution that the source of these intrauterine bacteria, whether they are alive, and their role, is not yet understood.  
During birth and rapidly thereafter, bacteria from the mother and the surrounding environment colonize the infant's gut.  The exact sources of bacteria is not fully understood, but may include the birth canal, other people (parents, siblings, hospital workers), breastmilk, food, and the general environment with which the infant interacts.  However, as of 2013, it remains unclear whether most colonizing arises from the mother or not.  Infants born by caesarean section may also be exposed to their mothers' microflora, but the initial exposure is most likely to be from the surrounding environment such as the air, other infants, and the nursing staff, which serve as vectors for transfer.  During the first year of life, the composition of the gut flora is generally simple and changes a great deal with time and is not the same across individuals.  The initial bacterial population are generally facultative anaerobic organisms investigators believe that these initial colonizers decrease the oxygen concentration in the gut, which in turn allows obligately anaerobic bacteria like Bacteroides, Actinobacteria, and Firmicutes to become established and thrive.  Breast-fed babies become dominated by bifidobacteria, possibly due to the contents of bifidobacterial growth factors in breast milk, and by the fact that breast milk carries prebiotic components, allowing for healthy bacterial growth.   In contrast, the microbiota of formula-fed infants is more diverse, with high numbers of Enterobacteriaceae, enterococci, bifidobacteria, Bacteroides, and clostridia. 
Caesarean section, antibiotics, and formula feeding may alter the gut microbiome composition.  Children treated with antibiotics have less stable, and less diverse floral communities.  Caesarean sections have been shown to be disruptive to mother-offspring transmission of bacteria, which impacts the overall health of the offspring by raising risks of disease such as celiacs, asthma, and type 1 diabetes.  This further evidences the importance of a healthy gut microbiome. Various methods of microbiome restoration are being explored, typically involving exposing the infant to maternal vaginal contents, and oral probiotics. 
When the study of gut flora began in 1995,  it was thought to have three key roles: direct defense against pathogens, fortification of host defense by its role in developing and maintaining the intestinal epithelium and inducing antibody production there, and metabolizing otherwise indigestible compounds in food subsequent work discovered its role in training the developing immune system, and yet further work focused on its role in the gut-brain axis. 
Direct inhibition of pathogens Edit
The gut flora community plays a direct role in defending against pathogens by fully colonising the space, making use of all available nutrients, and by secreting compounds that kill or inhibit unwelcome organisms that would compete for nutrients with it, these compounds are known as cytokines.  Different strains of gut bacteria cause the production of different cytokines. Cytokines are chemical compounds produced by our immune system for initiating the inflammatory response against infections. Disruption of the gut flora allows competing organisms like Clostridium difficile to become established that otherwise are kept in abeyance. 
Development of enteric protection and immune system Edit
In humans, a gut flora similar to an adult's is formed within one to two years of birth.  As the gut flora gets established, the lining of the intestines – the intestinal epithelium and the intestinal mucosal barrier that it secretes – develop as well, in a way that is tolerant to, and even supportive of, commensalistic microorganisms to a certain extent and also provides a barrier to pathogenic ones.  Specifically, goblet cells that produce the mucosa proliferate, and the mucosa layer thickens, providing an outside mucosal layer in which "friendly" microorganisms can anchor and feed, and an inner layer that even these organisms cannot penetrate.   Additionally, the development of gut-associated lymphoid tissue (GALT), which forms part of the intestinal epithelium and which detects and reacts to pathogens, appears and develops during the time that the gut flora develops and established.  The GALT that develops is tolerant to gut flora species, but not to other microorganisms.  GALT also normally becomes tolerant to food to which the infant is exposed, as well as digestive products of food, and gut flora's metabolites (molecules formed from metabolism) produced from food. 
The human immune system creates cytokines that can drive the immune system to produce inflammation in order to protect itself, and that can tamp down the immune response to maintain homeostasis and allow healing after insult or injury.  Different bacterial species that appear in gut flora have been shown to be able to drive the immune system to create cytokines selectively for example Bacteroides fragilis and some Clostridia species appear to drive an anti-inflammatory response, while some segmented filamentous bacteria drive the production of inflammatory cytokines.   Gut flora can also regulate the production of antibodies by the immune system.   One function of this regulation is to cause B cells to class switch to IgA. In most cases B cells need activation from T helper cells to induce class switching however, in another pathway, gut flora cause NF-kB signaling by intestinal epithelial cells which results in further signaling molecules being secreted.  These signaling molecules interact with B cells to induce class switching to IgA.  IgA is an important type of antibody that is used in mucosal environments like the gut. It has been shown that IgA can help diversify the gut community and helps in getting rid of bacteria that cause inflammatory responses.  Ultimately, IgA maintains a healthy environment between the host and gut bacteria.  These cytokines and antibodies can have effects outside the gut, in the lungs and other tissues. 
The immune system can also be altered due to the gut bacteria's ability to produce metabolites that can affect cells in the immune system. For example short-chain fatty acids (SCFA) can be produced by some gut bacteria through fermentation.  SCFAs stimulate a rapid increase in the production of innate immune cells like neutrophils, basophils and eosinophils.  These cells are part of the innate immune system that try to limit the spread of infection.
Without gut flora, the human body would be unable to utilize some of the undigested carbohydrates it consumes, because some types of gut flora have enzymes that human cells lack for breaking down certain polysaccharides.  Rodents raised in a sterile environment and lacking in gut flora need to eat 30% more calories just to remain the same weight as their normal counterparts.  Carbohydrates that humans cannot digest without bacterial help include certain starches, fiber, oligosaccharides, and sugars that the body failed to digest and absorb like lactose in the case of lactose intolerance and sugar alcohols, mucus produced by the gut, and proteins.  
Bacteria turn carbohydrates they ferment into short-chain fatty acids by a form of fermentation called saccharolytic fermentation.  Products include acetic acid, propionic acid and butyric acid.   These materials can be used by host cells, providing a major source of energy and nutrients.  Gases (which are involved in signaling  and may cause flatulence) and organic acids, such as lactic acid, are also produced by fermentation.  Acetic acid is used by muscle, propionic acid facilitates liver production of ATP, and butyric acid provides energy to gut cells. 
Gut flora also synthesize vitamins like biotin and folate, and facilitate absorption of dietary minerals, including magnesium, calcium, and iron.   Methanobrevibacter smithii is unique because it is not a species of bacteria, but rather a member of domain Archeae, and is the most abundant methane-producing archaeal species in the human gastrointestinal microbiota. 
Gut microbiota also serve as a source of Vitamins K and B12 that are not produced by the body or produced in little amount.  
The human metagenome (i.e., the genetic composition of an individual and all microorganisms that reside on or within the individual's body) varies considerably between individuals.   Since the total number of microbial and viral cells in the human body (over 100 trillion) greatly outnumbers Homo sapiens cells (tens of trillions), [note 1]   there is considerable potential for interactions between drugs and an individual's microbiome, including: drugs altering the composition of the human microbiome, drug metabolism by microbial enzymes modifying the drug's pharmacokinetic profile, and microbial drug metabolism affecting a drug's clinical efficacy and toxicity profile.   
Apart from carbohydrates, gut microbiota can also metabolize other xenobiotics such as drugs, phytochemicals, and food toxicants. More than 30 drugs have been shown to be metabolized by gut microbiota.  The microbial metabolism of drugs can sometimes inactivate the drug. 
Gut-brain axis Edit
The gut-brain axis is the biochemical signaling that takes place between the gastrointestinal tract and the central nervous system.  That term has been expanded to include the role of the gut flora in the interplay the term "microbiome-gut-brain axis" is sometimes used to describe paradigms explicitly including the gut flora.    Broadly defined, the gut-brain axis includes the central nervous system, neuroendocrine and neuroimmune systems including the hypothalamic–pituitary–adrenal axis (HPA axis), sympathetic and parasympathetic arms of the autonomic nervous system including the enteric nervous system, the vagus nerve, and the gut microbiota.  
A systematic review from 2016 examined the preclinical and small human trials that have been conducted with certain commercially available strains of probiotic bacteria and found that among those tested, Bifidobacterium and Lactobacillus genera (B. longum, B. breve, B. infantis, L. helveticus, L. rhamnosus, L. plantarum, and L. casei), had the most potential to be useful for certain central nervous system disorders. 
Effects of antibiotic use Edit
Altering the numbers of gut bacteria, for example by taking broad-spectrum antibiotics, may affect the host's health and ability to digest food.  Antibiotics can cause antibiotic-associated diarrhea by irritating the bowel directly, changing the levels of microbiota, or allowing pathogenic bacteria to grow.  Another harmful effect of antibiotics is the increase in numbers of antibiotic-resistant bacteria found after their use, which, when they invade the host, cause illnesses that are difficult to treat with antibiotics. 
Changing the numbers and species of gut microbiota can reduce the body's ability to ferment carbohydrates and metabolize bile acids and may cause diarrhea. Carbohydrates that are not broken down may absorb too much water and cause runny stools, or lack of SCFAs produced by gut microbiota could cause diarrhea. 
A reduction in levels of native bacterial species also disrupts their ability to inhibit the growth of harmful species such as C. difficile and Salmonella kedougou, and these species can get out of hand, though their overgrowth may be incidental and not be the true cause of diarrhea.    Emerging treatment protocols for C. difficile infections involve fecal microbiota transplantation of donor feces (see Fecal transplant).  Initial reports of treatment describe success rates of 90%, with few side effects. Efficacy is speculated to result from restoring bacterial balances of bacteroides and firmicutes classes of bacteria. 
The composition of the gut microbiome also changes in severe illnesses, due not only to antibiotic use but also to such factors as ischemia of the gut, failure to eat, and immune compromise. Negative effects from this have led to interest in selective digestive tract decontamination, a treatment to kill only pathogenic bacteria and allow the re-establishment of healthy ones. 
Antibiotics alter the population of the microbiota in the gastrointestinal tract, and this may change the intra-community metabolic interactions, modify caloric intake by using carbohydrates, and globally affects host metabolic, hormonal and immune homeostasis. 
There is reasonable evidence that taking probiotics containing Lactobacillus species may help prevent antibiotic-associated diarrhea and that taking probiotics with Saccharomyces (e.g., Saccharomyces boulardii ) may help to prevent Clostridium difficile infection following systemic antibiotic treatment. 
The gut microbiota of a woman changes as pregnancy advances, with the changes similar to those seen in metabolic syndromes such as diabetes. The change in gut microbiota causes no ill effects. The newborn's gut microbiota resemble the mother's first-trimester samples. The diversity of the microbiome decreases from the first to third trimester, as the numbers of certain species go up.  
Probiotics, prebiotics, synbiotics, and pharmabiotics Edit
Probiotics are microorganisms that are believed to provide health benefits when consumed.   With regard to gut microbiota, prebiotics are typically non-digestible, fiber compounds that pass undigested through the upper part of the gastrointestinal tract and stimulate the growth or activity of advantageous gut flora by acting as substrate for them.  
Synbiotics refers to food ingredients or dietary supplements combining probiotics and prebiotics in a form of synergism. 
The term "pharmabiotics" is used in various ways, to mean: pharmaceutical formulations (standardized manufacturing that can obtain regulatory approval as a drug) of probiotics, prebiotics, or synbiotics  probiotics that have been genetically engineered or otherwise optimized for best performance (shelf life, survival in the digestive tract, etc.)  and the natural products of gut flora metabolism (vitamins, etc.). 
There is some evidence that treatment with some probiotic strains of bacteria may be effective in irritable bowel syndrome and chronic idiopathic constipation. Those organisms most likely to result in a decrease of symptoms have included:
- Enterococcus faecium
- Lactobacillus plantarum
- Lactobacillus rhamnosus
- Propionibacterium freudenreichii
- Bifidobacterium breve
- Lactobacillus reuteri
- Lactobacillus salivarius
- Bifidobacterium infantis
- Streptococcus thermophilus
Tests for whether non-antibiotic drugs may impact human gut-associated bacteria were performed by in vitro analysis on more than 1000 marketed drugs against 40 gut bacterial strains, demonstrating that 24% of the drugs inhibited the growth of at least one of the bacterial strains. 
Bacteria in the digestive tract can contribute to and be affected by disease in various ways. The presence or overabundance of some kinds of bacteria may contribute to inflammatory disorders such as inflammatory bowel disease.  Additionally, metabolites from certain members of the gut flora may influence host signalling pathways, contributing to disorders such as obesity and colon cancer.  Alternatively, in the event of a breakdown of the gut epithelium, the intrusion of gut flora components into other host compartments can lead to sepsis. 
Helicobacter pylori infection can initiate formation of stomach ulcers when the bacteria penetrate the stomach epithelial lining, then causing an inflammatory phagocytotic response.  In turn, the inflammation damages parietal cells which release excessive hydrochloric acid into the stomach and produce less of the protective mucus.  Injury to the stomach lining, leading to ulcers, develops when gastric acid overwhelms the defensive properties of cells and inhibits endogenous prostaglandin synthesis, reduces mucus and bicarbonate secretion, reduces mucosal blood flow, and lowers resistance to injury.  Reduced protective properties of the stomach lining increase vulnerability to further injury and ulcer formation by stomach acid, pepsin, and bile salts.  
Bowel perforation Edit
Normally-commensal bacteria can harm the host if they extrude from the intestinal tract.   Translocation, which occurs when bacteria leave the gut through its mucosal lining, can occur in a number of different diseases.  If the gut is perforated, bacteria invade the interstitium, causing a potentially fatal infection.  : 715
Inflammatory bowel diseases Edit
The two main types of inflammatory bowel diseases, Crohn's disease and ulcerative colitis, are chronic inflammatory disorders of the gut the causes of these diseases are unknown and issues with the gut flora and its relationship with the host have been implicated in these conditions.     Additionally, it appears that interactions of gut flora with the gut-brain axis have a role in IBD, with physiological stress mediated through the hypothalamic–pituitary–adrenal axis driving changes to intestinal epithelium and the gut flora in turn releasing factors and metabolites that trigger signaling in the enteric nervous system and the vagus nerve. 
The diversity of gut flora appears to be significantly diminished in people with inflammatory bowel diseases compared to healthy people additionally, in people with ulcerative colitis, Proteobacteria and Actinobacteria appear to dominate in people with Crohn's, Enterococcus faecium and several Proteobacteria appear to be over-represented. 
There is reasonable evidence that correcting gut flora imbalances by taking probiotics with Lactobacilli and Bifidobacteria can reduce visceral pain and gut inflammation in IBD. 
Irritable bowel syndrome Edit
Irritable bowel syndrome is a result of stress and chronic activation of the HPA axis its symptoms include abdominal pain, changes in bowel movements, and an increase in proinflammatory cytokines. Overall, studies have found that the luminal and mucosal microbiota are changed in irritable bowel syndrome individuals, and these changes can relate to the type of irritation such as diarrhea or constipation. Also, there is a decrease in the diversity of the microbiome with low levels of fecal Lactobacilli and Bifidobacteria, high levels of facultative anaerobic bacteria such as Escherichia coli, and increased ratios of Firmicutes: Bacteroidetes. 
Other inflammatory or autoimmune conditions Edit
Allergy, asthma, and diabetes mellitus are autoimmune and inflammatory disorders of unknown cause, but have been linked to imbalances in the gut flora and its relationship with the host.  As of 2016 it was not clear if changes to the gut flora cause these auto-immune and inflammatory disorders or are a product of or adaptation to them.  
With asthma, two hypotheses have been posed to explain its rising prevalence in the developed world. The hygiene hypothesis posits that children in the developed world are not exposed to enough microbes and thus may contain lower prevalence of specific bacterial taxa that play protective roles.  The second hypothesis focuses on the Western pattern diet, which lacks whole grains and fiber and has an overabundance of simple sugars.  Both hypotheses converge on the role of short-chain fatty acids (SCFAs) in immunomodulation. These bacterial fermentation metabolites are involved in immune signalling that prevents the triggering of asthma and lower SCFA levels are associated with the disease.   Lacking protective genera such as Lachnospira, Veillonella, Rothia and Faecalibacterium has been linked to reduced SCFA levels.  Further, SCFAs are the product of bacterial fermentation of fiber, which is low in the Western pattern diet.   SCFAs offer a link between gut flora and immune disorders, and as of 2016, this was an active area of research.  Similar hypotheses have also been posited for the rise of food and other allergies. 
Diabetes mellitus type 1 Edit
The connection between the gut microbiota and diabetes mellitus type 1 has also been linked to SCFAs, such as butyrate and acetate. Diets yielding butyrate and acetate from bacterial fermentation show increased Treg expression.  Treg cells downregulate effector T cells, which in turn reduces the inflammatory response in the gut.  Butyrate is an energy source for colon cells. butyrate-yielding diets thus decrease gut permeability by providing sufficient energy for the formation of tight junctions.  Additionally, butyrate has also been shown to decrease insulin resistance, suggesting gut communities low in butyrate-producing microbes may increase chances of acquiring diabetes mellitus type 2.  Butyrate-yielding diets may also have potential colorectal cancer suppression effects. 
Obesity and metabolic syndrome Edit
The gut flora has also been implicated in obesity and metabolic syndrome due to the key role it plays in the digestive process the Western pattern diet appears to drive and maintain changes in the gut flora that in turn change how much energy is derived from food and how that energy is used.   One aspect of a healthy diet that is often lacking in the Western-pattern diet is fiber and other complex carbohydrates that a healthy gut flora require flourishing changes to gut flora in response to a Western-pattern diet appear to increase the amount of energy generated by the gut flora which may contribute to obesity and metabolic syndrome.  There is also evidence that microbiota influence eating behaviours based on the preferences of the microbiota, which can lead to the host consuming more food eventually resulting in obesity. It has generally been observed that with higher gut microbiome diversity, the microbiota will spend energy and resources on competing with other microbiota and less on manipulating the host. The opposite is seen with lower gut microbiome diversity, and these microbiotas may work together to create host food cravings. 
Additionally, the liver plays a dominant role in blood glucose homeostasis by maintaining a balance between the uptake and storage of glucose through the metabolic pathways of glycogenesis and gluconeogenesis. Intestinal lipids regulate glucose homeostasis involving a gut-brain-liver axis. The direct administration of lipids into the upper intestine increases the long chain fatty acyl-coenzyme A (LCFA-CoA) levels in the upper intestines and suppresses glucose production even under subdiaphragmatic vagotomy or gut vagal deafferentation. This interrupts the neural connection between the brain and the gut and blocks the upper intestinal lipids' ability to inhibit glucose production. The gut-brain-liver axis and gut microbiota composition can regulate the glucose homeostasis in the liver and provide potential therapeutic methods to treat obesity and diabetes. 
Just as gut flora can function in a feedback loop that can drive the development of obesity, there is evidence that restricting intake of calories (i.e., dieting) can drive changes to the composition of the gut flora. 
Liver disease Edit
As the liver is fed directly by the portal vein, whatever crosses the intestinal epithelium and the intestinal mucosal barrier enters the liver, as do cytokines generated there.  Dysbiosis in the gut flora has been linked with the development of cirrhosis and non-alcoholic fatty liver disease. 
Some genera of bacteria, such as Bacteroides and Clostridium, have been associated with an increase in tumor growth rate, while other genera, such as Lactobacillus and Bifidobacteria, are known to prevent tumor formation.  As of December 2017 there was preliminary and indirect evidence that gut microbiota might mediate response to PD-1 inhibitors the mechanism was unknown. 
Interest in the relationship between gut flora and neuropsychiatric issues was sparked by a 2014 study showing that germ-free mice showed an exaggerated HPA axis response to stress compared to non-GF laboratory mice.  As of January 2016, most of the work that has been done on the role of gut flora in the gut-brain axis had been conducted in animals, or characterizing the various neuroactive compounds that gut flora can produce, and studies with humans measuring differences between people with various psychiatric and neurological differences, or changes to gut flora in response to stress, or measuring effects of various probiotics (dubbed "psychobiotics in this context), had generally been small and could not be generalized whether changes to gut flora are a result of disease, a cause of disease, or both in any number of possible feedback loops in the gut-brain axis, remained unclear.  
A systematic review from 2016 examined the preclinical and small human trials that have been conducted with certain commercially available strains of probiotic bacteria and found that among those tested, the genera Bifidobacterium and Lactobacillus (B. longum, B. breve, B. infantis, L. helveticus, L. rhamnosus, L. plantarum, and L. casei) had the most potential to be useful for certain central nervous system disorders. 
The composition of the human gut microbiome is similar to that of the other great apes. However, humans’ gut biota has decreased in diversity and changed in composition since our evolutionary split from Pan.  Humans display increases in Bacteroidetes, a bacterial phylum associated with diets high in animal protein and fat, and decreases in Methanobrevibacter and Fibrobacter, groups that ferment complex plant polysaccharides.  These changes are the result of the combined dietary, genetic, and cultural changes humans have undergone since evolutionary divergence from Pan.
In addition to humans and vertebrates, some insects also possess complex and diverse gut microbiota that play key nutritional roles.  Microbial communities associated with termites can constitute a majority of the weight of the individuals and perform important roles in the digestion of lignocellulose and nitrogen fixation.  These communities are host-specific, and closely related insect species share comparable similarities in gut microbiota composition.   In cockroaches, gut microbiota have been shown to assemble in a deterministic fashion, irrespective of the inoculum  the reason for this host-specific assembly remains unclear. Bacterial communities associated with insects like termites and cockroaches are determined by a combination of forces, primarily diet, but there is some indication that host phylogeny may also be playing a role in the selection of lineages.  
For more than 51 years it has been known that the administration of low doses of antibacterial agents promotes the growth of farm animals to increase weight gain. 
In a study carried out on mice the ratio of Firmicutes and Lachnospiraceae was significantly elevated in animals treated with subtherapeutic doses of different antibiotics. By analyzing the caloric content of faeces and the concentration of small chain fatty acids (SCFAs) in the GI tract, it was concluded that the changes in the composition of microbiota lead to an increased capacity to extract calories from otherwise indigestible constituents, and to an increased production of SCFAs. These findings provide evidence that antibiotics perturb not only the composition of the GI microbiome but also its metabolic capabilities, specifically with respect to SCFAs. 
Gut Bacteria and Disease
Research suggests the gut bacteria in healthy people are different from those with certain diseases. People who are sick may have too little or too much of a certain type. Or they may lack a wide variety of bacteria. It’s thought some kinds may protect against ailments, while others may raise the risk.
Scientists have begun to draw links between the following illnesses and the bacteria in your gut:
Obesity, type 2 diabetes, and heart disease: Your gut bacteria affect your body’s metabolism. They determine things like how many calories you get from food and what kinds of nutrients you draw from it. Too much gut bacteria can make you turn fiber into fatty acids. This may cause fat deposits in your liver, which can lead to something called “metabolic syndrome” -- a condition that often leads to type 2 diabetes, heart disease, and obesity.
Inflammatory bowel diseases, including Crohn’s disease and ulcerative colitis: People with these conditions are believed to have lower levels of certain anti-inflammatory gut bacteria. The exact connection is still unclear. But it’s thought that some bacteria may make your body attack your intestines and set the stage for these diseases.
Colon cancer: Studies show that people with it have a different gut microbiota, including higher levels of disease-causing bacteria, than healthy people.
Anxiety, depression, and autism: The gut is packed with nerve endings that communicate with the brain. Your doctor may call this connection the “gut-brain axis.” Studies have suggested a link between gut bacteria and disorders of the central nervous system, like anxiety, depression, and autism spectrum disorder.
Arthritis: It’s thought that people with rheumatoid arthritis may have greater amounts of a bacteria linked to inflammation than people without it.
Role of the GI microbiota in health
Owing to its large genomic content and metabolic complement, the gut microbiota provides a range of beneficial properties to the host. Some of the most important roles of these microbes are to help to maintain the integrity of the mucosal barrier, to provide nutrients such as vitamins or to protect against pathogens. In addition, the interaction between commensal microbiota and the mucosal immune system is crucial for proper immune function.
Colonic bacteria express carbohydrate-active enzymes, which endow them with the ability to ferment complex carbohydrates generating metabolites such as SCFAs . Three predominant SCFAs, propionate, butyrate and acetate, are typically found in a proportion of 1:1:3 in the GI tract . These SCFAs are rapidly absorbed by epithelial cells in the GI tract where they are involved in the regulation of cellular processes such as gene expression, chemotaxis, differentiation, proliferation and apoptosis . Acetate is produced by most gut anaerobes, whereas propionate and butyrate are produced by different subsets of gut bacteria following distinct molecular pathways . Butyrate is produced from carbohydrates via glycolysis and acetoacetyl-CoA, whereas two pathways, the succinate or propanediol pathway, are known for the formation of propionate, depending on the nature of the sugar . In the human gut, propionate is mainly produced by Bacteroidetes, whereas the production of butyrate is dominated by Firmicutes [102,139,140]. For example, fermentation of starch by specialist Actinobacteria and Firmicutes, e.g. Eubacterium rectale or E. hallii, is thought to contribute significantly to butyrate production in the colon both directly and via metabolic cross-feeding . A. muciniphila is a key propionate producer specialised in mucin degradation . Propionate is primarily absorbed by the liver, whilst acetate is released into peripheral tissues . The role of SCFAs on human metabolism has recently been reviewed [140,143]. Butyrate is known for its anti-inflammatory and anticancer activities [140,143]. Butyrate is a particularly important energy source for colonocytes . A decreasing gradient of butyrate from lumen to crypt is suggested to control intestinal epithelial turnover and homeostasis by promoting colonocyte proliferation at the bottom of crypts, whilst increasing apoptosis and exfoliation of cells closer to the lumen . Butyrate can attenuate bacterial translocation and enhance gut barrier function by affecting tight-junction assembly and mucin synthesis . SCFAs also appear to regulate hepatic lipid and glucose homeostasis via complementary mechanisms. In the liver, propionate can activate gluconeogenesis, whilst acetate and butyrate are lipogenic . SCFAs also play a role in regulating the immune system and inflammatory response . They influence the production of cytokines, for example, stimulating the production of IL-18, an interleukin involved in maintaining and repairing epithelial integrity . Butyrate and propionate are histone deacetylase inhibitors that epigenetically regulate gene expression [140,143]. SCFAs have also been shown to modulate appetite regulation and energy intake via receptor-mediated mechanisms . Propionate has beneficial effects in humans acting on β-cell function  and attenuating reward-based eating behaviour via striatal pathways . Microbial metabolites other than SCFAs have been reported to have an impact on intestinal barrier functions, epithelium proliferation and the immune system .
The GI microbiota is also crucial to the de novo synthesis of essential vitamins which the host is incapable of producing . Lactic acid bacteria are key organisms in the production of vitamin B12, which cannot be synthesised by either animals, plants or fungi [149,150]. Bifidobacteria are main producers of folate, a vitamin involved in vital host metabolic processes including DNA synthesis and repair . Further vitamins, which gut microbiota have been shown to synthesise in humans, include vitamin K, riboflavin, biotin, nicotinic acid, panthotenic acid, pyridoxine and thiamine . Colonic bacteria can also metabolise bile acids that are not reabsorbed for biotransformation to secondary bile acids . All of these factors will influence host health. For example, an alteration of the co-metabolism of bile acids, branched fatty acids, choline, vitamins (i.e. niacin), purines and phenolic compounds has been associated with the development of metabolic diseases such as obesity and type 2 diabetes .
There are many lines of evidence in support of a role for the gut microbiota in influencing epithelial homeostasis . Germ-free mice exhibit impaired epithelial cell turnover which is reversible upon colonisation with microbiota . A role has been demonstrated for bacteria in promoting cell renewal and wound healing, for example, in the case of Lactobacilli rhamnosus GG . Furthermore, several species have been implicated in promoting epithelial integrity, such as A. muciniphila  and Lactobacillus plantarum . In addition to modulating epithelial properties, bacteria are proposed to modulate mucus properties and turnover. Mice housed under germ-free conditions have an extremely thin adherent colonic mucus layer, but when exposed to bacterial products (peptidoglycan or LPS), the thickness of the adherent mucus layer can be restored to levels observed in conventionally reared mice . B. thetaiotaomicron and F. prausnitzii have been implicated in the co-ordination of mucus production . R. gnavus E1, Lactobacillus casei DN-114 001 and B. thetaiotaomicron are able to remodel mucin glycosylation, for example, by modulating glycosyltransferase expression . It is proposed that these functions mediate the ability of other commensals or pathogens to colonise, potentially giving some commensal species a competitive advantage in the gut .
The GI microbiota is also important for the development of both the intestinal mucosal and systemic immune system as demonstrated by the deficiency in several immune cell types and lymphoid structures exhibited by germ-free animals. A major immune deficiency exhibited by germ-free animals is the lack of expansion of CD4+ T-cell populations. This deficiency can be completely reversed by the treatment of GF mice with polysaccharide A from the capsule of B. fragilis . This process is mainly performed via the pattern recognition receptors (PRRs) of epithelial cells, such as Toll-like or Nod-like receptors, which are able to recognise the molecular effectors that are produced by intestinal microbes. These effectors mediate processes that can ameliorate certain inflammatory gut disorders, discriminate between beneficial and pathogenic bacteria or increase the number of immune cells or PRRs . SFB, a class of anaerobic and clostridia-related spore-forming commensals present in the mammalian GI tract, actively interact with the immune system . Unlike other commensal bacteria, SFB are closely associated with the epithelial lining of the mammalian GI tract membrane, which stimulates epithelial cells to release serum amyloid A1 . Colonisation with SFB may also direct post-natal maturation of the gut mucosal lymphoid tissue, trigger a potent and broad IgA response, stimulate the T-cell compartment and up-regulate intestinal innate defence mediators, suggesting immune-stimulatory capacities of SFB (as reviewed in ). A. muciniphila has been correlated with protection against several inflammatory diseases [84,87,166], suggesting that this strain possesses anti-inflammatory properties although the underlying mechanisms have not been completely elucidated . Individuals with CD display mucosal dysbiosis characterised by reduced diversity of core microbiota and lower abundance of F. prausnitzii . F. prausnitzii monitoring may therefore serve as a biomarker to assist in gut disease diagnostics . Recently, an anti-inflammatory protein from F. prausnitzii was shown to inhibit the NF-㮫 pathway in intestinal epithelial cells and prevent colitis in an animal model .
The physical presence of the microbiota in the GI tract also influences pathogen colonisation by, for example, competing for attachment sites or nutrient sources, and by producing antimicrobial substances . Antibiotics have a profound impact on the microbiota that alter the nutritional landscape of the gut and lead to the expansion of pathogenic populations . For example, S. Typhimurium and C. difficile utilise fucose and sialic acid liberated by the gut microbiota, and increasing sialic acid levels post-antibiotic treatment favour their expansion within the gut . Enterohaemorrhagic E. coli has also been shown to access fucose or sialic acid liberated by the gut microbiota from mucins . Dietary fibre deficiency, together with a fibre-deprived, mucus-eroding microbiota, promotes greater epithelial access and lethal colitis by the mucosal pathogen Citrobacter rodentium in mice . The GI microbiota, via its structural components and metabolites, also stimulates the host to produce various antimicrobial compounds. These include AMPs such as cathelicidins, C-type lectins and (pro)defensins by the host Paneth cells via a PRR-mediated mechanism . The other mechanism by which the gut microbiota can limit pathogen overgrowth is by inducing mucosal SIgA . Induction of SIgAs directed against gut commensal bacteria occurs via an M-cell-mediated sampling mechanism . SIgAs are then anchored in the outer layer of colonic mucus through combined interactions with mucins and gut bacteria, thus providing immune protection against pathogens whilst maintaining a mutually beneficial relationship with commensals . PRR–MAMP (pattern recognition receptor–microbe-associated molecular patterns) cross-talk results in activation of several signalling pathways that are essential for promoting mucosal barrier function and production of AMPs, mucins and IgA, contributing to host protection against invading pathogens and preventing the overgrowth of the commensals themselves .
Gut bacteria instruct brain cells to fight inflammation
A newly discovered type of brain cell combats inflammation when it receives signals from bacteria in the gut. This finding — of research in animals — might lead to the development of probiotics that help reduce inflammation in people with neurological disorders such as multiple sclerosis (MS).
Star-shaped brain cells called astrocytes perform a wide range of maintenance services in the brain. These include providing nutrients to nerve cells and regulating the cells’ development.
When astrocytes malfunction, however, they can promote inflammation and neurodegeneration.
Research suggests that faulty astrocytes are involved in a range of neurodegenerative disorders, including Alzheimer’s and Parkinson’s diseases.
Now, a new study in mice has found that a previously unknown type of astrocyte actually protects against inflammation. More surprisingly, the cell steps up its anti-inflammatory work when it receives a molecular signal from gut bacteria.
“Over the years, many labs, including mine, have identified important roles for astrocytes in promoting neurological diseases,” says Dr. Francisco Quintana, of the Ann Romney Center for Neurologic Diseases, at Brigham and Women’s Hospital, in Boston, MA. Dr. Quintana is the senior and corresponding author of the new study.
He says this is the first known instance of astrocytes preventing inflammation.
“The reason we haven’t seen this before was because we were studying these cells as if they were uniform, or one single cell type,” Dr. Quintana explains. “But now we have the resolution to see the differences between these cells.”
It takes guts
Bacterial residents of the intestines may influence neurons and the brain through several routes.
Substances secreted by microbes into the gut may infiltrate blood vessels for a direct ride to the brain.
Microbes prompt neuropod cells in the gut lining to stimulate the vagus nerve, which connects directly to the brain.
More indirectly, microbes activate enteroendocrine cells in the gut lining, which send hormones throughout the body.
Even more indirectly, gut microbes influence immune cells and inflammation , which can affect the brain.
Extreme Diets Can Quickly Alter Gut Bacteria
With all the talk lately about how the bacteria in the gut affect health and disease, it's beginning to seem like they might be in charge of our bodies. But we can have our say, by what we eat. For the first time in humans, researchers have shown that a radical change in diet can quickly shift the microbial makeup in the gut and also alter what those bacteria are doing. The study takes a first step toward pinpointing how these microbes, collectively called the gut microbiome, might be used to keep us healthy.
"It's a landmark study," says Rob Knight, a microbial ecologist at the University of Colorado, Boulder, who was not involved with the work. "It changes our view of how rapidly the microbiome can change."
Almost monthly, a new study suggests a link between the bacteria living in the gut and diseases ranging from obesity to autism, at least in mice. Researchers have had trouble, however, pinning down connections between health and these microbes in humans, in part because it’s difficult to make people change their diets for the weeks and months researchers thought it would take to alter the gut microbes and see an effect on health.
But in 2009, Peter Turnbaugh, a microbiologist at Harvard University, demonstrated in mice that a change in diet affected the microbiome in just a day. So he and Lawrence David, now a computational biologist at Duke University in Durham, North Carolina, decided to see if diet could have an immediate effect in humans as well. They recruited 10 volunteers to eat only what the researchers provided for 5 days. Half ate only animal products—bacon and eggs for breakfast spareribs and brisket for lunch salami and a selection of cheeses for dinner, with pork rinds and string cheese as snacks. The other half consumed a high-fiber, plants-only diet with grains, beans, fruits, and vegetables. For the several days prior to and after the experiment, the volunteers recorded what they ate so the researchers could assess how food intake differed.
The scientists isolated DNA and other molecules, as well as bacteria, from stool samples from before, during, and after the experiment. In this way, they could determine which bacterial species were present in the gut and what they were producing. The researchers also looked at gene activity in the microbes.
Within each diet group, differences between the microbiomes of the volunteers began to disappear. The types of bacteria in the guts didn't change very much, but the abundance of those different types did, particularly in the meat-eaters, David, Turnbaugh, and their colleagues report online today in Nature. In 4 days, bacteria known to tolerate high levels of bile acids increased significantly in the meat-eaters. (The body secretes more bile to digest meat.) Gene activity, which reflects how the bacteria were metabolizing the food, also changed quite a bit. In those eating meat, genes involved in breaking down proteins increased their activity, while in those eating plants, other genes that help digest carbohydrates surfaced. "What was really surprising is that the gene [activity] profiles conformed almost exactly to what [is seen] in herbivores and carnivores," David says. This rapid shift even occurred in the long-term vegetarian who switched to meat for the study, he says. "I was really surprised how quickly it happened.”
From an evolutionary perspective, the fact that gut bacteria can help buffer the effects of a rapid change in diet, quickly revving up different metabolic capacities depending on the meal consumed, may have been quite helpful for early humans, David says. But this flexibility also has possible implications for health today.
"This is a very important aspect of a very hot area of science," writes Colin Hill, a microbiologist at University College Cork in Ireland, who was not involved with the work. "Perhaps by adjusting diet, one can shape the microbiome in a way that can promote health," adds Sarkis Mazmanian, a microbiologist at the California Institute of Technology in Pasadena, also unaffiliated with the study.
But how it should be shaped is still up in the air. "We're not yet at a point where we can make sensible dietary recommendations aimed at 'improving' the microbiota (and the host)," Hill writes. He and others are cautious, for example, about the implications of the increase seen in one bacteria, Bilophila wadsworthia, in the meat-eaters that in mice is associated with inflammatory bowel disease and high-fat diets. Says Knight, "There's still a long way to go before causality is established."
So Hill's best advice for now: "People should ideally consume a diverse diet, with adequate nutrients and micronutrients—whether it's derived from animal or plant or a mixed diet."